It would be good to have some documentation regarding deploying private repos using GitHub personal access tokens.
From what I understand it currently works as follows: when attempting to deploy a private repo, snakedeploy will ask for username and password. Use your github username as the username, and either your github password or the access token as the password. The GITHUB_TOKEN environment variable does not need to be set for this step, but is necessary at least the first time the contents of the repo are being fetched when running the snakemake workflow importing the workflow from the private repo, as documented here (use of GITHUB_TOKEN) and here (tagged versions of workflows being cached and to avoid downloading every time the workflow is being run).
If the above is correct, perhaps it would make sense to add something similar to the documentation?